System and method for isolating and analyzing cells

ABSTRACT

A system and method for isolating cells, comprising: a substrate having a broad surface; an array comprising a set of wells defined at the broad surface of the substrate, each well including: a base surface, an open surface directly opposing the base surface, defined at the broad surface of the substrate, and configured to receive one of a single cell and a single cluster of cells from a direction perpendicular to the broad surface of the substrate, and a set of channels that fluidly couple each well to at least one adjacent well; wherein the set of wells includes an interior subset and an exterior subset fluidly coupled to and surrounding the interior subset by way of the set of channels; and a fluid delivery module surrounding the array and fluidly coupled to each well in the set of wells.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.^(16/706,254), filed 6 Dec. 2019, which is a continuation of U.S.application Ser. No. 15/821,329, filed on 22 Nov. 2017, now issued asU.S. Pat. No. 10,533,229, which is a continuation of U.S. applicationSer. No. 14/289,155 filed on 28 May 2014, now issued as U.S. Pat. No.9,856,535, which claims the benefit of U.S. Provisional Application No.61/829,537 filed on 31 May 2013, each of which is incorporated in itsentirety by this reference.

TECHNICAL FIELD

This invention relates generally to the cell sorting field, and morespecifically to a new and useful system and method for isolating andanalyzing cells within the cell sorting field.

BACKGROUND

With an increased interest in cell-specific drug testing, diagnosis, andother assays, systems that allow for individual cell isolation,identification, and retrieval are becoming more desirable within thefield of cellular analysis. Furthermore, with the onset of personalizedmedicine, low-cost, high fidelity cellular sorting systems are becominghighly desirable. However, preexisting cell capture systems suffer fromvarious shortcomings that prevent widespread adoption for cell-specifictesting. For example, flow cytometry requires that the cell besimultaneously identified and sorted, and limits cell observation to asingle instance. Flow cytometry fails to allow for multiple analyses ofthe same cell, and does not permit arbitrary cell subpopulation sorting.Conventional microfluidic devices rely on cell-specific antibodies forcell selection, wherein the antibodies that are bound to themicrofluidic device substrate selectively bind to cells expressing thedesired antigen. Conventional microfluidic devices can also fail toallow for subsequent cell removal without cell damage, and only capturethe cells expressing the specific antigen; non-expressing cells, whichcould also be desired, are not captured by these systems. Cellularfilters can separate sample components based on size without significantcell damage, but suffer from clogging and do not allow for specific cellidentification, isolation of individual cells, and retrieval ofidentified individual cells. Other technologies in this field arefurther limited in their ability to allow multiplex assays to beperformed on individual cells, while minimizing sample preparationsteps.

Thus, there is a need in the cell sorting field to create a new anduseful cell system and method for isolating and analyzing cells.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic representation of an embodiment of a system forisolating and analyzing cells;

FIGS. 2A-2C depict variations of a portion of a system for isolating andanalyzing cells;

FIGS. 3A-3C depict variations of a portion of a system for isolating andanalyzing cells;

FIGS. 4A-4B depict example configurations of a portion of a system forisolating and analyzing cells;

FIG. 5 depicts a specific example of a system for isolating andanalyzing cells;

FIG. 6 depicts a variation of a system for isolating and analyzingcells;

FIGS. 7A and 7B depict additional portions of an embodiment of a systemfor isolating and analyzing cells;

FIG. 8 depicts a variation of a process involving a system for isolatingand analyzing cells;

FIG. 9 depicts an additional portion of an embodiment of a system forisolating and analyzing cells;

FIG. 10 depicts a specific example of a system for isolating andanalyzing cells;

FIG. 11 depicts an additional portion of an embodiment of a system forisolating and analyzing cells; and

FIG. 12 depicts a schematic representations of an embodiment of a methodfor isolating and analyzing cells;

DESCRIPTION OF THE PREFERRED EMBODIMENTS

The following description of the preferred embodiments of the inventionis not intended to limit the invention to these preferred embodiments,but rather to enable any person skilled in the art to make and use thisinvention.

1. System

As shown in FIG. 1, a system 100 for isolating and analyzing a set ofcells comprises: a substrate 105 having a broad surface; and an array110 including a set of wells 112 defined at the broad surface of thesubstrate, each well 113 in the set of wells 112 including a basesurface 120 defined within the substrate, an open surface 130 directlyopposing the base surface 120, and a set of channels 140 that fluidlycouple each well to every adjacent well in the set of wells. In somevariations, the system 100 can further include a perimeter channel 150surrounding the set of wells 112 and fluidly coupled to each well in anexterior subset 115 of the set of wells by way of at least one channelin the set of channels of each well in the exterior subset of the set ofwells. To facilitate sample or fluid delivery to the array 110, thesystem 100 can further include a fluid delivery module 170 configured tocouple to the substrate 105 and transfer a sample containing the set ofcells and/or another fluid to the array 110. Additionally oralternatively, the system 100 can include a cell removal module 180 thatextracts at least one of a single cell and a cell cluster from a well ofthe array. Additionally or alternatively, the system 100 can include anencapsulation module 190 configured to encapsulate the set of cells atthe array 110, and facilitate delivery of reagents to encapsulated cellsof the set of cells at the array 110.

The system 100 functions to isolate, capture, and retain cells of a cellpopulation, in at least one of single-cell format and single-clusterformat, at known, addressable locations, and further to facilitateperformance of multiple single-cell assays that can be performed onindividual cells (e.g., rare cells in a biological sample) or clustersof cells (e.g., doublets, triplets). Once cells are captured in definedlocations determined by single cell capture wells, a fluidic network ofthe system 100 can be used to provide and deliver reagentssimultaneously, sequentially, and/or in repetition to enable a varietyof cellular, sub-cellular or molecular reactions to be performed in eachof the single cells/cell clusters. The system 100 can also allow opticalinterrogation and detection of events on each of the captured cells at asingle cell/single cluster level. The system 100 can additionally oralternatively enable selective release and/or selective removal of oneor more of the captured cells for further processing and analysis. Insome embodiments, the system 100 can confer the benefits of real-timecell tracking, viable cell retrieval, and selective downstream molecularanalysis (e.g., electrophoresis), either in the same microfluidic chipor off-chip. In some embodiments, the system 100 can be used to capturecirculating tumor cells (CTCs) and subpopulations of CTCs, such ascirculating stem cells (CSCs), but can additionally or alternatively beused to capture any other suitable cell of possible interest. The system100 is preferably defined on a substrate, more preferably a microfluidicchip, but can alternatively be located on or defined by any suitablesubstrate.

The system 100 preferably achieves individual cell capture and retentionfrom a biological sample including a cell population, without antibodycoated wells, and preferably maintains the viability of the cellsthroughout isolation, capture, retention, and/or removal. Furthermore,the system 100 is preferably configured to prevent undesired fluidcurrents that can lift cells from the substrate or move cells/cellclusters from wells at which the cells were initially captured. However,in some variations, the system 100 can be configured to facilitatemoving of cells/cell clusters in any suitable manner. The flow path of afluid (e.g., biological sample, process reagent) through the system 100is preferably multi-directional and uniform, such that each cell/cellcluster in the system 100 experiences consistent conditions; however,the flow path can alternatively be unidirectional, bi-directional, orhave any other suitable characteristic(s). Cell sorting and viabilitymaintenance can additionally be accomplished by controlling the sampleflow rate through the system, or through any other suitable means.

In operation, the system 100 preferably receives a biological sampleincluding the cell population and facilitates distribution of thebiological sample uniformly across the array 110 (e.g., using smearing,using a cytospin procedure, etc.). However, the system 100 canadditionally or alternatively facilitate distribution of the biologicalsample across the array using positive pressure (e.g., positive pressureat an inlet to the array) and/or negative pressure (e.g., negativepressure at an outlet of the array). Additionally or alternatively,actuation pressure that facilitates sample distribution can be cycled ina pulse-width modulation fashion or sinusoidal fashion to provide netactuation pressure, either net positive at the inlet or net negative atthe outlet. As such, desired cells having a defining characteristic(e.g., size-based characteristic, density-based characteristic,adhesion-based characteristic, etc.) can be trapped within a well 113 asthe biological sample flows across the array 110. For example, in thevariation of the system 100 configured to capture CTCs, the wells 113are preferably configured based upon defining morpohological features ofCTC cells, in order to facilitate capture and retention of CTCs insingle cell or single cluster format. However, the system 100 canadditionally or alternatively be configured to retain and facilitateprocessing or any other suitable particle of interest in any othersuitable format.

1.1 System—Substrate

The substrate 105 has a broad surface 106, and functions to provide amedium at which the array 110 can be defined. The substrate 105 ispreferably composed of a rigid material with high transparency (e.g., atransparent material, a translucent material), in order to facilitateimaging of the substrate 105 to analyze captured single cells/cellclusters. In a few such variations, the substrate 105 can be composed ofany one or more of: glass, a silicone-based material, a polymer, and anyother suitable material with high transparency. Alternatively, thesubstrate 105 can be composed of any other suitable material having anyother suitable optical properties. In a few such variations, thesubstrate can be composed of any one or more of: a ceramic material, asemi-conducting material, a polymer, and any other suitable material.The substrate 105 composition can be configured to provide desiredcharacteristics relating to any one or more of: mechanicalcharacteristics (e.g., substrate mechanical properties as a mechanicalstimulus), optical properties (e.g., transparency), electricalproperties (e.g., conductivity), thermal properties (e.g., conductivity,specific heat, etc.), physical characteristics (e.g., wettability,porosity, etc.), and any other suitable characteristic. The substrate105 can be processed using any one or more of: etching methods, moldingmethods, printing methods (e.g., 3D printing processes), machiningmethods, and any other suitable manufacturing processes suited to abrittle, elastic, or ductile substrate material.

The broad surface 106 of the substrate 105 is preferably a planarsurface, such that microfluidic elements of the system 100 are definedat least partially at a planar surface. Alternatively, the broad surface106 of the substrate 105 can be a non-planar surface, as shown in FIG.2A-2C, such that microfluidic elements of the system 100 are defined atleast partially at a non-planar surface. In variations, the non-planarsurface can be a concave surface, a convex surface, or a surface havingconcave, planar, and/or convex surfaces. Such variations can facilitatevarious methods of depositing and distributing a sample at the array no.In any variations of the substrate 105 including a non-planar broadsurface 106, the non-planar portion(s) are preferably shallow (e.g.,having a small depth relative to a width of the broad surface) or short(e.g., having a small height relative to a width of the broad surface);however, the non-planar portion(s) can additionally or alternativelyinclude portions that are deep (e.g., having a large depth relative to awidth of the broad surface) or tall (e.g., having a large heightrelative to a width of the broad surface). In examples of a concavesurface, the concave surface can be any one or more of a semi-sphericalsurface, a semi-cylindrical surface, a parabolic surface, a pyramidalsurface, a conical surface, an ogive surface, a semi-ellipsoidalsurface, and any other suitable surface. In examples of a convexsurface, the convex surface can be any one or more of: semi-sphericalsurface, a semi-cylindrical surface, a parabolic surface, a pyramidalsurface, a conical surface, an ogive surface, a semi-elliopsoidalsurface, and any other suitable surface. In variations of the substrate105 including a non-planar broad surface 106, the non-planar broadsurface 106 preferably has a rotational axis of symmetry, for instance,to facilitate sample distribution by a cytospinning process. However,the surface can alternatively have any other suitable axis or type ofsymmetry, or can be asymmetrical. In any of these variations, thenon-planar surface of the broad surface 106 can be produced by any oneor more of: molding, by polishing, by spinning a material in a flowphase followed by setting the material, by machining, by printing (e.g.,3D printing), by etching, and by any other suitable process.

In a specific example, the array 110 is defined within a silicon moldusing a three mask photolithographic process and deep reactive ionetching (DRIE) process to etch microfluidic elements into the siliconmold. In the specific example, the etched elements of the silicon moldare then transferred polymethylmethacrylate (PMMA) sheets as a substrate105 using a hot embossing process. The substrate 105 in the specificexample has dimensions of 3 inches by 1 inch, in order to substantiallymatch dimensions of a glass microscope slide. In variations of thespecific example, and/or for other variations of the array 110, hotembossing of cyclic olefin polymer (COP) can be substituted for PMMA toform the microfluidic structures of the array no. However, the substrate105 can alternatively be any other suitable substrate 120 processed inany other suitable manner.

1.2 System—Array

The array 110 functions to capture the set of cells in addressable,known locations such that the set of cells can be individuallyidentified, processed, and analyzed. As such, the array 110 ispreferably configured to facilitate cell capture in at least one ofsingle-cell format and single-cluster format. As shown in FIG. 1, thearray 110 preferably includes a set of wells 112 defined at the broadsurface 106 of the substrate 105, each well 113 in the set of wells 112including a base surface 120 defined within the substrate, an opensurface 130 directly opposing the base surface 120, and a set ofchannels 140 that fluidly couple each well to at least one adjacent wellin the set of wells 112. In some variations, the array 100 can furtherinclude a perimeter channel 150 surrounding the set of wells 112 andfluidly coupled to each well 113 in an exterior subset 115 of the set ofwells 112 by way of at least one channel in the set of channels 140 ofeach well in the exterior subset 115 of the set of wells. Each substrate105 of the system 100 can have a single array 110, or can have multiplearrays 110 defined at the substrate in any suitable manner (e.g., in aradial configuration, in a rectangular configuration, in a linearconfiguration, in a curvilinear configuration, in a randomconfiguration, etc.).

The set of wells 112 functions to receive the set of cells in at leastone of single-cell format and single cluster format; however, the set ofwells 112 can additionally or alternatively be configured to receive anyother suitable type of particle, in any other suitable format. Each well113 in the set of wells 112 is preferably identical to every other wellin the set of wells 112, and includes a base surface 120 defined withinthe substrate 105, and an open surface 130 directly opposing the basesurface 120, defined at the broad surface 106 of the substrate 105. Thebase surface 120 is preferably parallel to the open surface 130;however, in some variations, the base surface 120 can alternatively benon-parallel to the open surface 130. Similar to the broad surface 106of the substrate 105, the base surface 120 can be a planar surface or anon-planar surface, and in variations of the base surface 120 having anon-planar surface, the non-planar surface can include convex and/orconcave portions having any suitable geometric characteristic.Additionally or alternatively, the base surface 120 can be any one ormore of: textured (e.g., to facilitate desired fluid flow behavior, toattract or repel a given particle type, etc.), characterized by adesired porosity, characterized by a desired surface treatment, andcharacterized by any other suitable feature that facilitates cellreception and/or retention in any other suitable manner.

The open surface 130 is preferably an opening in the substrate 105 thatprovides access to the base surface 120 of a well 113, and is configuredto receive one of a single cell and a single cluster of cells from adirection perpendicular to the broad surface 106 of the substrate 105.As such, the open surface 130 can have a characteristic dimension (e.g.,width, diameter) that is larger than, smaller than, or equal to that ofthe base surface 120. In an example for capture of circulating tumorcells (CTCs) from a sample in single-cell format, the characteristicdimension of either the base surface 120 or the open surface 130 can be25 microns, and in variations of the example, the characteristicdimension(s) can have any dimension from 0.5 microns to 50 microns. Inone example wherein the open surface 130 has a characteristic dimensionsmaller than that of the base surface 120, as shown in FIG. 3A, a well113 can have a lip 117 that forms a boundary of the open surface 130 inorder to provide a characteristic dimension that is smaller than that ofthe base surface 120. The lip 117 can be planar or non-planar, and canfurther facilitate retention of a single cell or a single cluster ofcells at the well 113. The open surface 130 can, however, include anyother suitable feature that facilitates cell reception and/or particleretrieval from the well 113 of the array 110.

In relation to the base surface 120 and the open surface 130, each well113 preferably has at least one wall 116 extending between the basesurface 120 and the open surface 130, as shown in FIG. 3A, wherein thewall 116 at least partially separates the well 113 from at least oneother adjacent well, defines a depth of the well, and is perpendicularto a plane defined by the open surface 130. The wall 116 can extendvertically from a plane defined by the open surface 130 to the basesurface 120; as such, in some variations, a well 113 of the array 100can be prismatic (e.g., cylindrical prismatic, polygonal prismatic,non-polygonal prismatic, etc.). However, the wall 116 can extend betweenthe open surface 130 and the base surface 120 in any other suitablemanner in other variations. For instance, the wall 116 can graduallyreduces a characteristic dimension of the well from the open surface tothe base surface (e.g., by forming steps, by gradually adjusting thecharacteristic dimension in a linear or a non-linear manner, etc.),examples of which are shown in FIGS. 3B and 3C. However, in somevariations, a well 113 may not have a well-defined wall 116perpendicular to a plane defined by the open surface 130 (e.g., the basesurface may extend in some manner directly to the open surface withoutforming a wall perpendicular to the open surface). In examples, the basesurface 120 and the open surface 130 can be separated, with or without awall, by a distance of between 0.5 microns to 50 microns (e.g., 25microns for an application involving capture of CTCs).

While every well 113 in the set of wells 112 can be substantiallyidentical, the set of wells 112 can alternatively include wells that arenon-identical to each other by any suitable feature (e.g., morphologicalfeature, mechanical feature, surface coating feature, thermalconductivity feature, electrical conductivity feature, etc.). As such,some variations of the system 100 can be configured to capture at leastone of multiple particle types and particles in multiple types offormats, in addressable locations, for processing and analysis. In afirst example, the array 110 can include a first subarray 118 with wellshaving a first characteristic dimension (e.g., well diameter) in orderto capture a first cell type in single cell format, and a secondsubarray 119 with wells having a second characteristic dimension (e.g.,well diameter) in order to capture a second cell type in single cellformat. In the first example, the first subarray 118 can be centrallylocated within the array no, and the second subarray 119 can beperipherally located within the array 110 and have a secondcharacteristic dimension that is smaller than the first characteristicdimension, in order to facilitate capture of larger particles at acentral portion of the array 110 and smaller particles at a peripheralportion of the array 100 (e.g., in a cytospin application). In onevariation of the first example, the array no can include wells having agradient of characteristic dimensions in a radial direction (e.g.,larger well dimensions toward the center of the array and smaller welldimensions toward the periphery of the array). In other variations ofthe first example, the array 110 can include wells having a gradient ofany other suitable feature characteristic (e.g., morphological feature,mechanical feature, surface coating feature, thermal conductivityfeature, electrical conductivity feature, etc.) in a radial direction.In other examples, the array 110 can include wells having a distribution(e.g., gradient) of any suitable feature characteristic (e.g.,morphological feature, mechanical feature, surface coating feature,thermal conductivity feature, electrical conductivity feature, etc.)along any suitable direction (e.g., linear direction, radial direction,circumferential direction, etc.).

Furthermore, the set of wells 112 is preferably arranged in a packedarray, but can alternatively be arranged in any other suitable manner.In one example, the set of wells 112 can be arranged in a packedrectangular array, as shown in FIG. 4A. In another example, the set ofwells 112 can be arranged in a closest packed array (e.g., hexagonalclosest packed array), as shown in FIG. 4B. In another example, the setof wells 112 can be arranged in any suitable irregular or non-uniformmanner, for instance, to facilitate fluid flow from one portion of thearray 110 to another portion of the array no. However, the set of wells112 can alternatively be arranged with any suitable spacing betweenwells (e.g., in a packed or a non-packed configuration), and in anyother suitable manner.

The set of channels 140 function to enable fluid flow exchange betweenat least two wells of the set of wells 112, and/or between one well ofthe set of wells 112 and another element of the system 100, whilepreventing migration of particle contents of a well 113 (e.g., acaptured cell, a captured cell cluster). As such, a characteristicdimension (e.g., width, diameter) of each channel 141 in the set ofchannels 140 for a well 113 is preferably smaller than a characteristicdimension (e.g., width, depth) of the well 113 in order to enableretention of desired contents of a well 113. In some alternativevariations, however, a well may be coupled to one or more channelshaving a characteristic dimension equal to or greater than that of acaptured cell/cell cluster, in order to facilitate migration of acell/cell cluster from one well to another well along a preferreddirection. A channel 141 of a set of channels can extend from the opensurface 130 of a well 113 to a base surface 120 of the well 113, suchthat a depth of the channel 141 is equal to the depth of the well 113.However, the channel(s) can alternatively have any other suitable depth(e.g., a depth less than that of the well) and be defined in relation tothe open surface 130 and the base surface 120 of a well 113 in any othersuitable manner. Preferably, every channel 141 in a set of channels 140is identical, for a given well 113, in morphology (e.g., length, crosssection); however, a set of channels 140 for a well 113 canalternatively include one or more non-identical channels 141 (e.g., achannel having a different length, a channel having a different crosssection than other channels in a set of channels). The set of channels140 can be arranged about a well 113 in a uniform radial pattern, can bearranged about a well 113 in a non-uniform radial pattern, or can bearranged about a well 113 in any other suitable manner to couple thewell 133 to its adjacent well(s). However, in some variations, the setof channels 140 can be configured to couple each well to two adjacentwells (aside from an initial well and a terminal well, which would eachonly include a single channel), such that the set of wells 112 iscoupled in series. In some variations, the channel(s) of a set ofchannels 140 can be defined within a region of the substrate 105 betweenadjacent wells, or can be defined by overlapping portions of adjacentwells, as shown in FIG. 5. In a specific example, a channel 141 can havea characteristic dimension of 5 microns, and in variations of thespecific example, a channel 141, can have a characteristic dimensionranging from 0.5 microns to 50 microns. Alternatively, at least one well113 in the set of wells 112 may not be coupled to every adjacent well invariations of the array 110. Furthermore, some variations of the arraymay not include a set of channels 140 for any well 113 of the set ofwells 112.

As shown in FIGS. 1, 5, and 6, the system 100 can further include aperimeter channel 150 surrounding the set of wells 112 and fluidlycoupled to each well 113 in an exterior subset 115 of the set of wellsby way of at least one channel 141 in the set of channels 140 of eachwell in the exterior subset 115 of the set of wells 112. The perimeterchannel 150 functions to enable modulation of an amount of fluid at thearray 110, such that an amount of fluid within the array 110 can bereduced, maintained, or increased by way of the perimeter channel 150.As such, the perimeter channel 150 can receive and distribute processreagents throughout the array 110, and/or facilitate removal of excessor used process reagents from the array 110. The perimeter channel 150can be at least partially enclosed by the substrate 105 or anotherelement of the system 100, and coupled to a fluid port 151 thatfacilitates modulation of an amount of fluid at the array. As such,fluid can be delivered and/or removed from the array 110 by way of thefluid port 151, in an automatic or manual manner (e.g., using a pump,using capillary soaking, etc.). Additionally or alternatively, theperimeter channel 150 can include open portions not enclosed by thesubstrate 105 that facilitate fluid level modulation with or without useof the fluid port(s), for instance, using capillary soaking orevaporation. In some variations, the perimeter channel 150 can becoupled to any other suitable portion of the array 110 (e.g., anon-exterior subset of the array), in order to facilitate modulation ofan amount of fluid at the array 110.

In some variations of the system 100, one or more wells of the array 110can further include any other suitable element that facilitatesstimulation and/or detection of a parameter (e.g., a cellular responseparameter) at the well(s) of the array 110. In one example, one or morewells of the set of wells 112 of the array 110 can include an electrodeembedded in the substrate 105 at a surface of the well 113 in order tofacilitate detection of bioelectrical signals from contents of the well113, and/or to facilitate stimulation of the contents of the well 113.In variations of the example, the electrode can be embedded with anexposed portion at least one of the base surface 120 and a wall 116 ofthe well 113. In other examples, the well(s) can be coupled to channelsthat facilitate delivery of process reagents to a cell/cell cluster at awell 113, or facilitate extraction of contents of a well 113 (e.g.,processed intracellular contents) from the well 113. The system 100 can,however, include any other suitable element that facilitates processingand/or analysis of cells in at least one of single-cell format andsingle cluster format.

1.3 System—Fluid Delivery Module

Also shown in FIGS. 1, 7A, and 7B, the system 100 can include a fluiddelivery module 170 configured to couple to the substrate 105. The fluiddelivery module 170 functions to transfer a sample containing the set ofcells and/or another fluid to the array 110. As shown in FIGS. 7A and7B, the fluid delivery module 170 can include a first plate 171configured proximal the broad surface of the substrate 105, a secondplate 172 configured proximal a surface of the substrate 105, directlyopposing the broad surface of the substrate 105, and a clamping moduleconfigured to couple the first plate 171 to the second plate 172,thereby positioning and/or aligning the substrate 105 between the firstplate 171 and the second plate 172. Alternatively, however, the firstplate 171 can be directly coupled to the substrate 105 and/or to anyother suitable element of the system 100, such that the fluid deliverymodule 170 omits a second plate 172. As such, the fluid delivery module170 facilitates positioning of the substrate 105 to receive and/or sealthe sample or fluid at the array 110 (e.g., with a compressive force,with a hermetic seal, etc.). Additionally or alternatively, the fluiddelivery module 170 can include an absorbant layer 173 configuredbetween the first plate 171 and the substrate 105, that facilitatesmodulation of an amount of fluid at the array 110.

As shown in FIG. 7A, the first plate 171 can have a rectangularfootprint that spans the broad surface 106 of the substrate 105.However, the first plate 171 can alternatively have any other suitablefootprint (e.g., non-rectangular footprint, circular footprint,ellipsoidal footprint, etc.) configured to span all or a portion of thebroad surface 106 of the substrate 105. The first plate 171 preferablyhas a recess 174 facing the broad surface 106 of the substrate 105,wherein the recess 174 functions as a reservoir to temporarily hold asample and/or a processing reagent proximal to the array 110. As such,the recess 174 preferably spans the array 110, and aligns with the arraywhen the first plate 171 is coupled to the substrate 105. In onevariation, the recess 174 can be a rectangular recess defined within thesurface of the first plate 171 facing the substrate 105. Furthermore,the recess can have a substantially planar base surface 176, as shown inFIG. 7A, or any other suitable base surface 176 (e.g., non-planar basesurface). However, the recess 174 can alternatively have any othersuitable morphology. Additionally or alternatively, the recess 174 caninclude a sealing element (e.g., o-ring, sealant, etc.) surrounding aregion of the recess 174 proximal the substrate 105, in order to providea hermetic seal upon coupling of the first plate 171 to the substrate105. However, the first plate 171 can alternatively be configured in anyother suitable manner.

The second plate 172 is configured proximal to a surface of thesubstrate 105, directly opposing the broad surface of the substrate 105,and functions to provide a base to which the first plate 171 can becoupled, thereby positioning the substrate 105 between the first plate171 and the second plate 172. The second plate 172 preferably provides acomplementary surface to which the surface of the substrate 105,opposing the broad surface 106, can be coupled. In one variation, thesecond plate 172 is a substantially planar, in order to provide asurface to which a planar surface of the substrate 105 (e.g., a planarsurface directly opposing the broad surface of the substrate) can becoupled; however, the second plate 172 can be configured relative to thesubstrate 105 in any other suitable manner. Furthermore, the secondplate 172 can include an aligning element that facilitates alignment ofthe second plate 172 relative to the substrate 105 and/or to the firstplate 172. In variations, the aligning element can include any one ormore of: a protrusion and/or a recess at the second plate 172 thatfacilitates alignment, a track that facilitates alignment, a magneticelement, and any other suitable alignment element.

In one variation, the first plate 171 is preferably coupled to thesecond plate with a coupling mechanism that can include one or more of:a pin, a screw, a magnetic coupler, a clamp, and any other suitablecoupling mechanism. To prevent obstruction, the coupling mechanism canbe located at peripheral portions of the system (e.g., at peripheralportions of the first plate 171, the second plate 172, and/or thesubstrate 105), or at any other suitable location that does notinterfere with function of the substrate. Alternatively, some variationsof the system 100 may omit the second plate 172, and have directcoupling between the first plate 171 and the substrate 105 in anysuitable manner.

Some variations of the fluid delivery module 170 can include anabsorbant layer 173 situated between the first plate 171 and thesubstrate 105. The absorbant layer 173 functions to facilitatemodulation of an amount of fluid at the array 110, during a process thatdistributes the cells/cell clusters in single cell and/or cluster formatat the array. As such, the absorbant layer 173 can be composed of anysuitable absorbant material configured to absorb liquids, withoutreceiving or retaining target cells of the sample. In some variations,the absorbant material can include any one or more of: a hydrogel havinga network with pore sizes smaller than a characteristic dimension of atarget cell, a porous material (e.g., a sponge), a hydrophilic material,and any other suitable absorbant material. Additionally oralternatively, in some variations, the absorbant layer 173 can beconfigured to attract, receive, and/or retain undesired particles from asample, such that that the absorbant material facilitates filtration orsegregation of undesired particles from the target particles of asample. In such variations, the absorbant layer 173 can be configured toreceive or retain undesired particles according to affinitymolecule-based capture, pore size-based capture, adhesion behavior,and/or any other suitable mechanism.

As shown in FIG. 7A, the absorbant layer 173 is preferably a planarlayer 173 in contact with both the first plate 171 and the substrate 105upon coupling of the first plate 171 to align the recess 174 with thearray 110. However, the absorbant layer 173 can alternatively have anyother suitable morphology. Additionally, the absorbant layer 173preferably has an opening 177 aligned with the recess 174 of the firstplate 171, such that fluid within the reservoir formed by the recess 174can reach the array 110 through the opening 177 of the absorbant layer173. The opening can be a single opening, or can comprise any suitablenumber of openings that provide access between contents of the recess174 and the array 110 of the substrate 110. However, the abosrbant layer173 can alternatively be configured in any other suitable manner.

In one example application, as shown in FIG. 8, an assembly 199comprising the first plate 171, the absorbant layer 173, the substrate105, and the second plate 172 can be coupled together and rotated aboutan axis of rotation parallel to and offset from the broad surface of thesubstrate 105, such that the normal defined by the broad surface 106 ofthe substrate 105 passes through the axis of rotation. As such, duringrotation of the assembly 199, fluid within a reservoir formed by therecess 174 of the first plate 171 can be pushed toward the wells of thearray 110 by centripetal force (e.g., to capture cells at the wells),while excess fluid can flow into the absorbant layer 173. However, invariations of the example application, the assembly 199 can be rotatedabout any other suitable axis, and/or capturing of cells at the array110 can be performed in any other suitable manner.

1.4 System—Cell Removal Module

Also shown in FIGS. 1 and 9, the system 100 can further include a cellremoval module 180 that functions to extract at least one of a singlecell and a cell cluster from a well 113 of the array. While anindividual cell from a single well 113 is preferably selectivelyremoved, the cell removal module 180 can facilitate simultaneousmultiple cell/cell cluster removal from the array 110. The cell/cellcluster is preferably removed by applying a removal force to the cell.The removal force is preferably applied by aspirating the contents outof a well 113 (i.e., using a negative pressure); however, the removalforce can additionally or alternatively be applied by pumping fluidthrough the array 110 (e.g., by way of a perimeter channel 150) toprovide a positive pressure that drives the cell/cell cluster from thewell 113. In one variation, the pump pressure provided by a pumpmechanism at the cell removal module 180 is less than 10,000 Pa, and ina specific variation, the provided pump pressure is 6,000 Pa. However,any other suitable pump or aspiration pressure can be used.

In some variations, the cell removal module 180 can comprise a cellremoval tool 181. The cell removal tool 181 functions to selectivelyremove one or more isolated cells from an addressable location withinthe system 100. The cell removal tool 181 is preferably configured toremove a cell/cell cluster from a single well 113, but can alternativelybe configured to simultaneously remove multiple cells/cell clusters frommultiple wells 113.

In a first variation of the cell removal tool 181, the cell removal tool181 is configured to access the array no from a direction normal to thebroad surface 106 of the substrate 105. The cell removal tool 181preferably removes the cell/cell cluster in a substantially normaldirection from the broad surface 106 of the substrate 105, but canalternatively remove the cell/cell cluster in an angled directionrelative to the broad surface 106 of the substrate 105. The cell removaltool 181 preferably includes a hollow channel (e.g., of a micropipette)that accesses the array 110 and defines a substantially fluidly isolatedvolume in fluid communication with one or more wells. The hollow channelcan include one or more sealing elements at the tip 182 (e.g., apolymeric coating or adequate geometry) that facilitate fluid sealformation with the well(s) 113. The cell removal tool 181 preferablytapers from a proximal end to the tip 181, in order to provide anadequate geometry to receive contents of a well 113 into the cellremoval tool 181; however, the cell removal tool 181 can alternativelyhave any other suitable form. As such, the hollow needle is preferablyconfigured to form a substantially fluidly isolated volume within a well113 of interest, and a low-pressure generator (e.g., a pump) is thenused to aspirate the retained cell/cell cluster out of the well 113,through the hollow channel, and into a cell collection volume of thecell removal tool 181. In one variation, the cell removal tool 181 is amicropipette having a height of 200 micrometers and a hollow channeldiameter of 25 micrometers; however, other variations of the specificexample can have any other suitable defining dimensions.

The cell removal tool 181 can be manufactured using microfabricationtechniques, or can additionally or alternatively be injection molded,laser cut, stamped, or manufactured using any other suitablemanufacturing technique. In one variation of hollow needle manufacture,a lumen is preferably etched into a substrate 110, such as silicon,using etching techniques such as deep reactive ion etching (DRIE),plasma etching, or any other suitable etching method. This step ispreferably utilized with a mask that covers the portions of thesubstrate 110 to be protected. The walls and associated profiles arethen preferably manufactured through isotropic etching of the substrate110 utilizing a corrosive liquid or plasma, but any other suitableisotropic material removal method can be used. A mask is preferably usedto protect the puncture end. Multiple hollow needles are preferablysimultaneously manufactured as an array 200, but can alternatively beindividually manufactured. The cell removal tool 181 can, however,comprise any other suitable cell removal tool such as that described inU.S. application Ser. No. 13/557,510, entitled “Cell Capture System andMethod of Use” and filed on 25 Jul. 2012, which is herein incorporatedin its entirety by this reference.

Cell removal from the system 100 is preferably automated, but canadditionally or alternatively be semi-automated or manual. Furthermore,cell removal can be performed along with cell identification, comprisingautomatic fixing, permeabilzation, staining, imaging, and identificationof the cells removed from the array 110 through image analysis (e.g.,through visual processing with a processor, by using a light detector,etc.) or in any other suitable manner. The cell removal module 180 canbe configured to facilitate advancement of a cell removal tool 181 to awell 113 containing a cell/cell cluster of interest, for instance, withan actuation subsystem. The cell removal module 180 can additionally oralternatively be configured to facilitate cell removal method selectionand/or cell removal tool selection. In another variation, cellidentification at the cell removal module 180 can be semi-automated, andcell retrieval can be automated. For example, cell staining and imagingcan be done automatically, wherein identification and selection of thecells of interest can be done manually. In another variation, all stepscan be performed manually. However, any combination of automated ormanual steps can be used.

1.5 System—Encapsulation Module

Additionally or alternatively, the system 100 can include anencapsulation module 190 configured to encapsulate the set of cells atthe array 110, and facilitate delivery of reagents to encapsulated cellsof the set of cells at the array 110. In one variation, theencapsulation module 190 can include a first encapsulation layer 191coupled to the substrate 105 proximal the broad surface 106 of thesubstrate 105, that functions to seal cells captured at the set of wells112 within an encapsulation matrix 199. As such, the first encapsulationlayer 191 can form a boundary opposing the base surfaces 120 of eachwell 113 in the set of wells 112. The first encapsulation layer 191 ispreferably an optically clear laminate, in order to facilitatevisualization of contents of the array 110; however, the firstencapsulation layer 191 can alternatively comprise any other suitablematerial. Furthermore, the first encapsulation layer 191 can bereversibly removed and/or applied to the array 110, in order tofacilitate access to encapsulated contents of the set of wells 112.

In one variation, as shown in FIGS. 10 and 11, an encapsulation matrix199 can be flowed into the array 110 with the encapsulation module 190at any suitable portion of the array 110, forming an encapsulationvolume 198 spanning the set of wells 112 and the set of channels 140 foreach well 113 in the set of wells 112, up to the first encapsulationlayer 191. The encapsulation matrix 199 preferably isolates a well 113within an array 110. The encapsulation matrix 501 preferably has a flowstate and a set state, wherein any one or more of: a photochemicalreaction, phase transition, thermochemical reaction, polymerizationreaction and any other suitable reaction switches the encapsulationmatrix 199 from the flow state to the set state. In the flow state, theencapsulation matrix 199 is preferably substantially viscous, such thatthe encapsulation matrix 199 does not flow into the wells 113 duringintroduction into the system 100. In the set state, the encapsulationmatrix 199 is preferably a solid or gel that prevents particle egressfrom the wells 113 (e.g., egress of cells and/or large nucleic acidmolecules from the pores), and is preferably porous or selectivelypermeable to permit small molecule, buffer, and reagent penetrationtherethrough. In one variation, the encapsulation matrix 199 is amicroporous agarose gel, and in another variation, the encapsulationmatrix 199 is a photopolymerizable hydrogel, such as PEG orpolyacrylamide with photoinitiator; however, the encapsulation matrix199 can alternatively be any suitable material with any other suitablepolymerization agent.

In some variations, the encapsulation module 190 can additionallyinclude a second encapsulation layer 192 forming the base surfaces 120of the set of wells 112 of an array, such that the base surfaces 120 arenot directly defined within the substrate 105, but at the secondencapsulation layer 192. As such, the second encapsulation layer 192 canform a second boundary defining the base surfaces 120 of each well 113in the set of wells 112, thereby partially bounding the encapsulationvolume 198. The second encapsulation layer 192 is preferably anoptically clear laminate, in order to facilitate visualization ofcontents of the array 110; however, the second encapsulation layer 192can alternatively comprise any other suitable material. Furthermore, thesecond encapsulation layer 192 can be reversibly removed and/or appliedto the array 110, in order to facilitate access to encapsulated contentsof the set of wells 112.

Preferably, as shown in FIGS. 10 and 11, the encapsulation module 190 isconfigured such that diffusion of one or more reagents through theencapsulation volume 198 occurs upon removal of the second encapsulationlayer 192 (e.g., in a direction from the base surface of a well towardthe open surface of the well) from the substrate 105; however, theencapsulation module can additionally or alternatively be configuredsuch that diffusion of one or more reagents through the encapsulationvolume 198 occurs upon removal of the first encapsulation layer 191(e.g., in a direction from the open surface of the well toward the basesurface of the well) from the substrate 105. As such, removal of one orboth of the first encapsulation layer 191 and the second encapsulationlayer 192 from the substrate 105 can provide access of one or morereagents, through the encapsulation matrix 199, to captured contents atthe set of wells 112. In examples, such processing reagents can includeany one or more of: stains (e.g., cell-specific stains), cocktails(e.g., antibody cocktails), lysing reagents, fixing reagents,permeabilization reagents, culture reagents (e.g., media), and any othersuitable process reagent. The reagent(s) can be delivered through theencapsulation volume 198 by applying pressure (e.g., positive pressure,negative pressure) and/or by passive diffusion. However, theencapsulation module 190 can alternatively be configured in any othersuitable manner.

1.6 System—Specific Examples

In a first specific example, as shown in FIG. 5, the system 100′includes an array 110′ of 250,000 wells arranged in an rectangularpacked array, wherein each well 113′ is coupled to every adjacent wellby a fluid channel formed at the overlap between adjacent wells. In thefirst specific example, each well in the array 110′ has a diameter of 25microns (e.g., a circumscribed diameter) and a depth of 25 microns, asdefined between the base surface 120 and the open surface 130 of eachwell 113′. The array 110′ of the first specific example can receive asample volume from 0.1 to 10 milliliters in volume; however, othervariations of the first specific example can receive any other suitablesample volume. In the first specific example, every fluid channel 141′of a set of fluid channels 140′ for each well 113′ has a width of 5microns, in order to enable cell/cell cluster retention, while allowingfluid exchange. In the first specific example, the substrate 105′ iscoupled between a first plate 171 and a second plate 172, with anabsorbant layer 173 situated between the first plate 171 and thesubstrate 105′. The absorbant layer has a rectangular opening 177aligned with a rectangular recess 174 of the first plate 171, in orderto facilitate fluid flow from a reservoir formed by the recess 174through the opening 177. Other variations of the first specific examplecan, however, include any other suitable elements that facilitatecell/cell cluster capture, retention, processing, sorting, and/oranalysis in any other suitable manner.

In a second specific example, as shown in FIG. 10, the system 100″includes an array 110″ of 414 wells 113″ arranged in series, whereineach well 113″ (aside from an initial well and a terminal well) iscoupled to two adjacent wells in series by fluid channels 141″ definedat regions between adjacent wells. In the second specific example, theinitial well and the terminal well are each only coupled to one adjacentwell in the set of wells 112 by way of fluid channels 141″. In thesecond specific example, the set of wells 112 is arranged in aboustrophedonic pattern, but variations of the second specific examplecan include arrangement of the set of wells 112 in any other suitablemanner (e.g., serpentine pattern, spiral pattern, linear pattern,curvilinear pattern, etc.). In the second specific example, each well inthe array 110″ has a diameter of 1.1 millimeters (e.g., a circumscribeddiameter) and a depth of 1 millimeter, as defined between the basesurface 120 and the open surface 130 of each well 113″, in order todefine an approximately 1 milliliter volume capacity for each well. Inthe second specific example, every fluid channel 141″ of a set of fluidchannels 140″ for each well 113″ has a cross section of 250 microns×250microns, and is configured proximal the open surfaces 130″ of the set ofwells 112, in order to enable cell/cell cluster retention, whileallowing fluid exchange. Furthermore, in the second specific example, awell 113″ is spaced from an adjacent well in the set of wells 112″ by aspacing of 2 millimeters. In the second specific example, the substrate105″ is coupled between a first encapsulation layer 191 and a secondencapsulation layer 192, each comprising an optically clear laminate,and wherein the second encapsulation layer 192″ forms the base surfaces120 of the set of wells 112. Upon delivery of an encapsulation matrix199 into the array 110″ and transitioning of the encapsulation matrix199 to a set state, the second encapsulation layer 192 of theencapsulation module 190 is removed to allow passive diffusion throughthe encapsulation matrix 199 and to encapsulated contents of the set ofwells 112. Other variations of the first specific example can, however,include any other suitable elements that facilitate cell/cell clustercapture, retention, processing, sorting, and/or analysis in any othersuitable manner.

Additionally or alternatively, the system 100 can include any othersuitable element that facilitates cell processing and/or analysis. Forinstance, the system 100 can include optical elements (e.g., embeddedwithin the substrate 105, coupled to the substrate 105) that function tofacilitate imaging. The optical elements function to adjust incominglight, preferably to facilitate imaging. The optical elements canfunction to bend, reflect, collimate, focus, reject, or otherwise adjustthe incoming light. The optical elements are preferably defined withinthe substrate 105, but can alternatively be defined by any othersuitable component of the system 100. Optical elements can include anyone or more of: light reflectors disposed within the substrate thicknessadjacent the array(s) 110 defined on a surface of the substrate 105opposite that defining the array 110, microlenses defined on a broadsurface of the substrate 105 proximal that defining the array 110, lightcollimators, light polarizers, interference filters, light reflectors(e.g., 90° illumination elements), elements that minimize excitationrays from going into path of collected fluorescence emission light,diffraction filters, light diffusers, and any other suitable opticalelement. The system 100 can additionally or alternatively include wellaffinity mechanisms that function to attract a cell of interest 10towards a well 113. Well affinity mechanisms can include electric fieldtraps, affinity moieties (e.g., coated to a well surface), features(e.g., microfluidic features) that direct flow into an element, or anyother suitable pore affinity mechanism. The system 100 can, however,include any other suitable element(s).

Additionally, as a person skilled in the field of cell sorting willrecognize from the previous detailed description and from the figuresand claims, modifications and changes can be made to the embodiments,variations, examples, and specific applications of the system 100described above without departing from the scope of the system 100.

2. Method

As shown in FIG. 12, a method 200 for isolating and analyzing a set ofcells comprises: distributing a biological sample including a cellpopulation throughout an array comprising a set of wells defined at thebroad surface of a substrate, each well of the set of wells including abase surface, an open surface directly opposing the base surface,defined at the broad surface of the substrate, and configured to retainone of a single cell and a single cluster of cells of the cellpopulation, and a set of channels that fluidly couple each well to atleast one adjacent well in the set of wells S210; modulating an amountof fluid of the biological sample from the array S220; receiving aprocess reagent at the array, thereby facilitating diffusive delivery ofthe process reagent to the cell population in at least one ofsingle-cell format and single-cluster format S230; transmitting heat,through the substrate, to the cell population S240; and analyzingintracellular content of the cell population, processed with the processreagent at the array, thereby facilitating analysis of the cellpopulation in at least one of single-cell format and single-clusterformat S250. The method 200 can additionally or alternatively includeany one or more of: encapsulating the set of cells at the array withinan encapsulation matrix S260; and diffusing a second process reagentacross the encapsulation matrix and through at least one of the basesurface and the open surface S270.

The method 200 functions to enable isolation, capture, and retention ofcells, more preferably cells in single-cell format and/or single-clusterformat, at known, addressable locations, and further to facilitateperformance of multiple single-cell/single cluster assays that can beperformed on individual cells or cell clusters (e.g., rare cells in abiological sample). The method 200 is preferably implemented at least inpart using the system 100 described in Section 1 above; however themethod 200 can additionally or alternatively be implemented using anyother suitable system 100 for cell capture and analysis. In someembodiments, the method 200 can be used to capture and facilitateanalyses of circulating tumor cells (CTCs) and subpopulations of CTCs,such as circulating stem cells (CSCs), but can additionally oralternatively be used to capture any other suitable cell of possibleinterest for processing and analysis.

Block S210 recites: distributing a biological sample including a cellpopulation throughout an array comprising a set of wells defined at thebroad surface of a substrate, each well of the set of wells including abase surface, an open surface directly opposing the base surface,defined at the broad surface of the substrate, and configured to retainone of a single cell and a single cluster of cells of the cellpopulation, and a set of channels that fluidly couple each well to atleast one adjacent well in the set of wells. Block S210 functions toreceive a biological sample including target cells of interest at anembodiment of the system 100 described in Section 1 above, and tofacilitate distribution of the target cells into wells of the system 100in at least one of single-cell format and single-cluster format.However, Block S210 can alternatively include receiving a biologicalsample at any other suitable system configured to capture cells in atleast one of single-cell format and single-cluster format. In variationsof Block S210, the biological sample can be received directly at avariation of the array (e.g., by pipetting, by fluid delivery through afluid channel coupled to the array), at the array by way of a variationof the first plate of a fluid delivery module (e.g., from a reservoirdefined by a recess of the first plate, from a fluid channel coupled tothe first plate, from a fluid channel embedded within the first plateand in fluid communication with the array, etc.), and/or in any othersuitable manner. Furthermore, in variations of Block S210, the cellpopulation can include a cell population of target cells (e.g., CTCs,CSCs) and/or any other suitable particle of interest.

In variations of Block S210, distributing can include any one or moreof: cytospinning the substrate with the biological sample about an axisparallel to the broad surface of the substrate, cytospinning thesubstrate with the biological sample about an axis perpendicular to thebroad surface of the substrate, cytospinning the substrate with thebiological sample about an axis oriented at any suitable angle relativeto the broad surface of the substrate, smearing the biological sample atthe array of the substrate, depositing the biological sample at thearray under positive and/or negative pressure (e.g., by way of a pumpingmechanism), incubating the biological sample at the array for a periodof time, and in any other suitable manner of sample deposition anddistribution. Furthermore, in applications of Block S210 includingcytospinning, an axis of rotation can be offset from any suitablereference point of the substrate, in any suitable manner. In onespecific application, as shown in FIG. 8, Block S210 includes rotatingan assembly comprising a first plate coupled to a second plate and withthe substrate and an absorbant layer between the first plate and thesecond plate, about an axis of rotation parallel to and offset from thebroad surface of the substrate, such that the normal defined by thebroad surface of the substrate passes through the axis of rotation. Assuch in the specific example, during rotation of the assembly, fluidwithin a reservoir formed by a recess of the first plate can be pushedtoward the wells of the array by centripetal force (e.g., to capturecells at the wells), while excess fluid can flow into the absorbantlayer. In the specific application, the assembly is rotated at anangular velocity from 500-2000 revolutions per minute; however, othervariations of the specific application can include rotation of any othersuitable assembly at any other suitable angular velocity. Furthermore,in variations of the specific application, the assembly can be rotatedabout any other suitable axis, and/or capturing of cells at the arraycan be performed in any other suitable manner.

Block S220 recites: modulating an amount of fluid of the biologicalsample at the array, which functions to increase, decrease, or maintainan amount of fluid, from the biological sample, at the array, therebyfacilitating capture of cells at the array in at least one ofsingle-cell format and single-cluster format. Block S220 preferablyincludes reducing an amount of fluid at the array; however, Block S220can additionally or alternatively include increasing or maintaining anamount of fluid at the array. In variations, Block S220 can includemodulating the amount of fluid by any one or more of: applying negativeand/or positive pressure at the array (e.g., at a pump coupled to thesystem 100), using capillary soaking, by evaporation (e.g., using aheating element of the system, by passive evaporation), and any othermeans of modulating an amount of fluid at the array. In one variation,Block S220 can include providing an absorbant layer at the array,configured to absorb excess fluid at the array by capillary soaking. Ina specific example of this variation, the absorbant layer can include anopening aligned with the array, as described in Section 1 above, whereincytospinning of a substrate including the array simultaneously forcescells into the set of wells of the array in at least one of single-cellformat and single-cluster format and facilitates flow of excess fluidinto the absorbant layer. As such, in some variations, Block S220 can beperformed simultaneously with Block S210 (e.g., in cytospinningapplications), or can alternatively be performed prior to or after BlockS210.

Block S230 recites: receiving a process reagent at the array, therebyfacilitating diffusive delivery of the process reagent to the cellpopulation in at least one of single-cell format and single-clusterformat. The process reagent can include any one or more of: a lysingreagent, a fixing reagent, a permeabilization reagent, a stain, areagent for immunochemistry, a reagent for an in-situ hybridizationassay (e.g., a fluorescence in-situ hybridization assay, FISH) fornucleic acids (e.g., DNA, RNA, mRNA, etc.), a reagent for polymerasechain reaction (PCR), a culture reagent (e.g., media) for cellmaintenance and/or subsequent harvesting from the array, and any othersuitable reagent. In variations, the process reagent(s) can be deliveredto and distributed across the array in a manner similar to that ofdistributing the biological sample at the array in variations of BlockS210. Additionally or alternatively, the amount(s) of the processreagent(s) at the array can be modulated in a manner similar to that ofmodulating fluid as in variations of Block S220. However, receiving theprocess reagent(s) and/or modulating the amount(s) of the processreagent(s) can additionally or alternatively be performed in any othersuitable manner.

Block S240 recites: transmitting heat, through the substrate, to thecell population captured at the array, which functions to providecontrolled incubation and/or thermocycling of the cell population withthe process reagent(s) received in variations of Block S230. Block S240preferably includes providing uniform heating at each well of the set ofwells of the array; however, Block S240 can alternatively includeproviding heat non-uniformly across the array (e.g., providing heat witha gradient to examine effects of different heating parameters on thecell population). In variations, Block S240 can include contacting thesubstrate with at least one heating element, adjusting an environmentaltemperature of the substrate, or transmitting heat throughout thesubstrate by way of heating elements coupled to or embedded within thesubstrate. However, transmitting heat through the substrate canadditionally or alternatively be performed in any other suitable manner.Transmitting heat thus includes incubating the substrate, with the cellpopulation and a process reagent for a desired amount of time at adesired temperature, according to parameters suited for the processreagent(s) provided in Block S230. As such, transmitting heat canfacilitate one or more of: lysing the cell population, fixing the cellpopulation, permeabilizing the cell population, staining the cellpopulation, performing immunochemistry for the cell population, bindinga probe to intracellular nucleic acid content of the cell population, asin an in-situ hybridization assay (e.g., a fluorescence in-situhybridization assay, FISH), performing polymerase chain reaction fornucleic acid content of the cell population, culturing the cellpopulation, and any other suitable application.

In variations of the method 200, Blocks S220, S230, and/or S240 can beperformed with any suitable number of repetitions, according toprotocols for processing the cell population according to differentassays. For instance, removing excess fluid can be performed prior toand/or after heating the substrate, in order to remove excess processreagent(s) from the array after they are no longer needed. Furthermore,Blocks S220, S230, and/or S240 can be performed in any suitable order orsimultaneously, according to protocols for processing the cellpopulation according to different assays.

Block S250 recites: analyzing intracellular content of the cellpopulation, processed with the process reagent at the array, therebyfacilitating analysis of the cell population in at least one ofsingle-cell format and single-cluster format. In variations, Block S250can include any one or more of: harvesting contents of the set of wells(e.g., cells, intracellular content), culturing cells captured at theset of wells, detecting biomarkers exhibited by the cell population(e.g., using fluorescent detection), performing a quantitative analysis(e.g., a quantitative analysis of mRNA expression), characterizing acell phenotype (e.g., a cancer cell phenotype) based upon biomarkerexpression, providing a recommended therapy based upon characterizationof a cell phenotype, performing flow cytometry with captured cells ofthe cell population, and performing any other suitable analysis. Theanalyses performed in variations can thus be performed for cells withinand/or harvested from the array.

As shown in FIG. 12, the method 200 can additionally or alternativelyinclude Block S260, which recites: encapsulating the set of cells at thearray within an encapsulation matrix. Block S230 functions to isolatecaptured cells of interest at the set of wells, in order to facilitatefurther processing and analysis of the set of cells in at least one ofsingle-cell format and single-cluster format. The encapsulation matrixpreferably isolates a well and its contents within the array, in anembodiment of the system 100 described above; however, the encapsulationmatrix can isolate particles in any other manner and/or in any othersuitable system. The encapsulation matrix preferably has a flow stateand a set state, wherein a photochemical reaction, thermochemicalreaction, polymerization reaction and/or any other suitable reactionswitches the encapsulation matrix from the flow state to the set state.In the flow state, the encapsulation matrix is preferably substantiallyviscous, such that the encapsulation matrix does not flow into the poresduring introduction into the system 100. In the set state, theencapsulation matrix is preferably a solid or gel that prevents particleegress from the pores 111 (e.g., egress of cells, reagent particles, andlarge nucleic acid molecules from the pores), and is preferably porousor selectively permeable to permit small molecule, buffer, and reagent(e.g., detergent, enzyme, primer, etc.) penetration therethrough.Furthermore, by changing the constituents of a buffer or reagent andallowing sufficient time for diffusion, specific reagents/buffers can beentered into or eluted out from encapsulated cells. In one variation,the encapsulation matrix is a microporous agarose gel with a low meltingpoint, and in another variation, the encapsulation matrix is aphotopolymerizable hydrogel, such as PEG or polyacrylamide withphotoinitiator; however, the encapsulation matrix can alternatively beany suitable material with any other suitable polymerization agent.

In relation to the system 100 described in Section 1 above, theencapsulation matrix can isolate contents of the set of wells between atleast one of a first encapsulation layer and a second encapsulationlayer, such that Block S260 includes delivering the encapsulation matrixinto a fluidic network defined between the substrate, the firstencapsulation layer, and/or the second encapsulation layer in a flowstate prior to setting the encapsulation matrix. As such, variations ofBlock S260 can include delivering the encapsulation matrix to the arraythrough an opening that provides access to the array (e.g., a fluidport), or in any other suitable manner.

Also shown in FIG. 12, the method 200 can additionally or alternativelyinclude Block S270, which recites: diffusing a second process reagentacross the encapsulation matrix S270 and through at least one of thebase surface and the open surface of a well of the array. The secondprocess reagent can include any one or more of: a lysing reagent, afixing reagent, a permeabilization reagent, a stain, a reagent forimmunochemistry, a reagent for an in-situ hybridization assay (e.g., afluorescence in-situ hybridization assay, FISH) for nucleic acids (e.g.,DNA, RNA, mRNA, etc.), a reagent for polymerase chain reaction (PCR), aculture reagent (e.g., media) for cell maintenance and/or subsequentharvesting from the array, and any other suitable reagent, as in BlockS230. The second process reagent is preferably diffused across theencapsulation matrix, to contents of the set of wells through the basesurfaces of the wells of the set of wells, but can additionally oralternatively be diffused across the encapsulation matrix, to contentsof the set of wells through the open surfaces of the wells of the set ofwells. As such, in relation to the system 100 described in Section 1above, Block S250 can include removing at least one of the secondencapsulation layer and the first encapsulation layer, and providing areagent at the exposed surface(s) of the substrate to facilitatediffusing of the second process reagent(s) into the wells of the array.Block S250 preferably includes delivering the second process reagent(s)uniformly to each well of the set of wells of the array; however, BlockS250 can alternatively include delivering the second process reagent(s)non-uniformly to the set of wells of the array. Furthermore, Block S250can additionally or alternatively include actively driving the secondprocess reagent(s) across the encapsulation matrix, for instance, byproviding pressure (e.g., positive pressure, negative pressure) at thearray or by providing centripedal force at the array.

The method 200 can additionally or alternatively include any othersuitable steps or blocks that facilitate reception, processing, and/oranalysis of the cell population in at least one of single-cell formatand single-cluster format.

2. Method—Specific Applications

In a first specific application, the method 200 is configured tofacilitate automated FISH analysis of intracellular DNA of a cellpopulation (e.g., from a patient) at an embodiment of the system 100described in Section 1 above. Furthermore, variations of the firstspecific application can include performing immunochemistry followingperformance of the FISH analysis, in order to characterize the cellpopulation. The first specific application can thus facilitaterecommendation of therapies target to the patient providing a biologicalsample including the cell population, in a patient-specific manner. Insome examples, the therapies can include Herceptin for Her-2 positivepatients, and Xalkori for ALK-positive non-small cell lung cancerpatients.

In a second specific application, the method 200 is configured tofacilitate automated FISH analysis of intracellular mRNA of a cellpopulation (e.g., from a patient) at an embodiment of the system 100described in Section 1 above, in order to characterize the cellpopulation. In the second specific example, the FISH analysis includesquantitative analysis of mRNA expression for each cell, includingmultiplexing of multiple biomarkers (e.g., 6 biomarkers) for each cellusing a set of fluorophores provided in a suitable process reagent.

In a third specific application, the method 200 is configured tofacilitate FISH analysis of intracellular mRNA of a cell population(e.g., from a patient) at an embodiment of the system 100 described inSection 1 above. Furthermore, variations of the third specificapplication can include performing immunochemistry in combination withperformance of the FISH analysis, in order to characterize the cellpopulation. In an example, SUM159 breast cancer cells, pre-selected forCD44+ and CD24− antibodies, and isolated in at least one of single-cellformat and single-cluster format can be analyzed with immunochemistryand FISH assays in the third specific application.

In a fourth specific application, the method 200 is configured tofacilitate capture of viable cancer cells at an embodiment of the system100 described in Section 1 above. In the fourth specific application,the captured cells are then harvested from the array after a period ofincubation, for use in applications including drug discovery testing,sequencing of cells (e.g., CTCs), and development of improved cancercell characterization assays.

The system 100 and method 200 of the preferred embodiment and variationsthereof can be embodied and/or implemented at least in part as a machineconfigured to receive a computer-readable medium storingcomputer-readable instructions. The instructions are preferably executedby computer-executable components preferably integrated with the systemand one or more portions of a processor and/or a controller. Thecomputer-readable medium can be stored on any suitable computer-readablemedia such as RAMs, ROMs, flash memory, EEPROMs, optical devices (CD orDVD), hard drives, floppy drives, or any suitable device. Thecomputer-executable component is preferably a general or applicationspecific processor, but any suitable dedicated hardware orhardware/firmware combination device can alternatively or additionallyexecute the instructions.

The FIGURES illustrate the architecture, functionality and operation ofpossible implementations of systems, methods and computer programproducts according to preferred embodiments, example configurations, andvariations thereof. In this regard, each block in the flowchart or blockdiagrams may represent a module, segment, or portion of code, whichcomprises one or more executable instructions for implementing thespecified logical function(s). It should also be noted that, in somealternative implementations, the functions noted in the block can occurout of the order noted in the FIGURES. For example, two blocks shown insuccession may, in fact, be executed substantially concurrently, or theblocks may sometimes be executed in the reverse order, depending uponthe functionality involved. It will also be noted that each block of theblock diagrams and/or flowchart illustration, and combinations of blocksin the block diagrams and/or flowchart illustration, can be implementedby special purpose hardware-based systems that perform the specifiedfunctions or acts, or combinations of special purpose hardware andcomputer instructions.

As a person skilled in the art will recognize from the previous detaileddescription and from the figures and claims, modifications and changescan be made to the preferred embodiments of the invention withoutdeparting from the scope of this invention defined in the followingclaims.

We claim:
 1. A method for isolating and analyzing a population of cellsin single-cell format, the method comprising: providing a devicecomprising: a substrate having a broad surface and a set of wellsdefined at the broad surface of the substrate, wherein each well in theset of wells comprises: a base surface defined within the substrate, andan open surface directly opposing the base surface, each well sized toreceive a single target cell of the population of cells from a directionperpendicular to the broad surface of the substrate; capturing thepopulation of cells in single-cell format, such that each captured celland associated cell-derived contents of the population of cells can beidentified and addressed in addressable locations corresponding to theset of wells; encapsulating cells captured at the set of wells with anencapsulation material; delivering a set of process reagents to the setof wells, with diffusion of the set of process reagents through theencapsulation material to contents of the set of wells; performing a setof single-cell processing operations, in-situ, upon contents of the setof wells; and detecting optical signals from contents of the set ofwells through at least one of the encapsulation material and thesubstrate, wherein the optical signals represent results of the set ofsingle-cell processing operations.
 2. The method of claim 1, wherein theset of wells is arranged in a hexagonal close packed configuration. 3.The method of claim 1, wherein the set of processing reagents comprisesone or more of: a stain, a cocktail, a lysing reagent, a fixing reagent,a permeabilization reagent, a culture reagent, an immunochemistryreagent, an in-situ hybridization reagent, and a polymerase chainreaction reagent.
 4. The method of claim 1, wherein the encapsulationmaterial comprises a polymer material with a polymerization agent. 5.The method of claim 1, wherein the encapsulation material comprises oneof: an agarose, a polyacrylamide material, a hydrogel material, and apolyethylene glycol-derived material.
 6. The method of claim 1, whereinencapsulating cells captured at the set of wells with the encapsulationmaterial comprises permitting diffusion of the set of process reagentsto the set of wells, while preventing egress of captured cells andmolecules above a threshold size from the set of wells.
 7. The method ofclaim 6, wherein preventing egress comprises preventing egress ofnucleic acid material, derived from captured target cells of thepopulation of target cells, from the set of wells and through theencapsulation layer.
 8. The method of claim 1, wherein the set ofsingle-cell processing operations comprises one of: immunochemistry, DNAfluorescence in-situ hybridization (FISH), and mRNA FISH.
 9. The methodof claim 1, wherein the substrate is transparent, such that detectingoptical signals from contents of the set of wells comprises detectingoptical signals through the substrate.
 10. The method of claim 1,wherein the encapsulation layer is transparent, such that detectingoptical signals from contents of the set of wells comprises detectingoptical signals through the encapsulation layer.
 11. The method of claim1, further comprising contacting the substrate with a heating element,thereby uniformly transmitting heat to contents of the set of wellsthrough the substrate.
 12. The method of claim 11, wherein uniformlytransmitting heat comprises incubating captured target cells of thepopulation of cells within the set of wells.
 13. The method of claim 1,further comprising positioning a plate adjacent to the substrate andproviding a gap between the plate and the set of wells of the substrate.14. The method of claim 13, wherein encapsulating cells captured at theset of wells with the encapsulation material comprises transmitting theencapsulation material in a flow state through the gap, andtransitioning the encapsulation material to a set state.
 15. The methodof claim 1, further comprising delivering a target cell of thepopulation of target cells into a cell removal module, upon applicationof a force to contents of a well of the set of wells.
 16. The method ofclaim 1, wherein each of the set of wells comprises a first set of fluidchannels configured for fluid exchange within the system, the methodfurther comprising diffusing one or more of the set of process reagentsthrough each of the set of wells by way of the first set of fluidchannels.
 17. The method of claim 1, wherein the device furthercomprises a fluid delivery module fluidly coupled to each well of theset of wells by a set of channels, wherein each of the set of channelscomprises an identical length.
 18. The method of claim 1, whereindetecting optical signals comprises detecting fluorescence-based signalsresulting from reactions between one or more of the set of processreagents and contents captured at the set of wells.
 19. The method ofclaim 1, wherein the set of wells comprises at least 250,000 individualwells.
 20. The method of claim 1, wherein each of the set of wells has adepth of at least 25 microns.